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All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

A HARD GAMMA-RAY FLARE FROM 3C 279 IN 2013 DECEMBER

The blazar 3C 279 exhibited twin γ-ray flares of similar intensity in 2013 December and 2014 April. In this work, we present a detailed multi-wavelength analysis of the 2013 December flaring event. Multi-frequency observations reveal the uncorrelated variability patterns with X-ray and optical–UV fluxes peaking after the γ-ray maximum. The broadband spectral energy distribution (SED) at the peak of the γ-ray activity shows a rising γ-ray spectrum but a declining optical–UV flux. This observation along with the detection of uncorrelated variability behavior rules out the one-zone leptonic emission scenario. We, therefore, adopt two independent methodologies to explain the SED: a time-dependent lepto-hadronic modeling and a two-zone leptonic radiative modeling approach. In the lepto-hadronic modeling, a distribution of electrons and protons subjected to a randomly orientated magnetic field produces synchrotron radiation. Electron synchrotron is used to explain the IR to UV emission while proton synchrotron emission is used to explain the high-energy γ-ray emission. A combination of both electron synchrotron self-Compton emission and proton synchrotron emission is used to explain the X-ray spectral break seen during the later stage of the flare. In the two-zone modeling, we assume a large emission region emitting primarily in IR to X-rays and γ-rays to come primarily from a fast-moving compact emission region. We conclude by noting that within a span of four months, 3C 279 has shown the dominance of a variety of radiative processes over each other and this reflects the complexity involved in understanding the physical properties of blazar jets in general.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Reconstruction of Six-Dimensional Phase Space

A phase space is a mathematical representation of all possible physical states of a system. Particle beams at Fermilab exist within a six-dimensional (6D) phase space defined by three positional components, (x, y, z) and three momentum components, (px, py, pz). To reconstruct this space implies taking measurement data from detectors and mapping out particle behavior using computational methods. The beam detectors, however, are only able to detect spatial distribution among the events of the beam, therefore being limited to positional data. Also, due to the vast number of events in a particle beam, it is extremely difficult to analyze and differentiate every single one’s behavior. However, with Machine Learning (ML), which can distinguish between patterns and map out particle behavior more efficiently. We first used the particle beam software, G4beamline, to simulate a 10,000-event muon beam, adjusting parameters such as initial momentum magnitude (p¬0) and virtual detector position. Using ten virtual detectors, we analyzed p0 values such that minimum 9,990 events were analyzed by every detector. We then input the data from these beam simulations to a C++ program, that randomly selects 100 events, and creates a 2D histogram based on spatial distribution, detector position, and event intensity. This process is repeated 100 times to create 100 histograms per p0 value. These images were then input to a modified ResNet18 Convolutional Neural Network (CNN) for training, and to predict p0 from some unseen set of histograms. The model was accurate when trained on momentum increments of 5 MeV/c and provided with denser training samples around highly variable test values. These results displayed machine learning being able to accurately predict p0 from being trained on different particle behaviors.

Shirlee, Jermain [Fermilab]↗
DOE OSTI2013

Evaluating IMRT and VMAT dose accuracy: Practical examples of failure to detect systematic errors when applying a commonly used metric and action levels

Purpose: This study (1) examines a variety of real-world cases where systematic errors were not detected by widely accepted methods for IMRT/VMAT dosimetric accuracy evaluation, and (2) drills-down to identify failure modes and their corresponding means for detection, diagnosis, and mitigation. The primary goal of detailing these case studies is to explore different, more sensitive methods and metrics that could be used more effectively for evaluating accuracy of dose algorithms, delivery systems, and QA devices.Methods: The authors present seven real-world case studies representing a variety of combinations of the treatment planning system (TPS), linac, delivery modality, and systematic error type. These case studies are typical to what might be used as part of an IMRT or VMAT commissioning test suite, varying in complexity. Each case study is analyzed according to TG-119 instructions for gamma passing rates and action levels for per-beam and/or composite plan dosimetric QA. Then, each case study is analyzed in-depth with advanced diagnostic methods (dose profile examination, EPID-based measurements, dose difference pattern analysis, 3D measurement-guided dose reconstruction, and dose grid inspection) and more sensitive metrics (2% local normalization/2 mm DTA and estimated DVH comparisons).Results: For these case studies, the conventional 3%/3 mm gamma passing rates exceeded 99% for IMRT per-beam analyses and ranged from 93.9% to 100% for composite plan dose analysis, well above the TG-119 action levels of 90% and 88%, respectively. However, all cases had systematic errors that were detected only by using advanced diagnostic techniques and more sensitive metrics. The systematic errors caused variable but noteworthy impact, including estimated target dose coverage loss of up to 5.5% and local dose deviations up to 31.5%. Types of errors included TPS model settings, algorithm limitations, and modeling and alignment of QA phantoms in the TPS. Most of the errors were correctable after detection and diagnosis, and the uncorrectable errors provided useful information about system limitations, which is another key element of system commissioning.Conclusions: Many forms of relevant systematic errors can go undetected when the currently prevalent metrics for IMRT/VMAT commissioning are used. If alternative methods and metrics are used instead of (or in addition to) the conventional metrics, these errors are more likely to be detected, and only once they are detected can they be properly diagnosed and rooted out of the system. Removing systematic errors should be a goal not only of commissioning by the end users but also product validation by the manufacturers. For any systematic errors that cannot be removed, detecting and quantifying them is important as it will help the physicist understand the limits of the system and work with the manufacturer on improvements. In summary, IMRT and VMAT commissioning, along with product validation, would benefit from the retirement of the 3%/3 mm passing rates as a primary metric of performance, and the adoption instead of tighter tolerances, more diligent diagnostics, and more thorough analysis.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2018

Novel antibody reagents for characterization of drug- and tumor microenvironment-induced changes in epithelial-mesenchymal transition and cancer stem cells

The presence of cancer stem cells (CSCs) and the induction of epithelial-to-mesenchymal transition (EMT) in tumors are associated with tumor aggressiveness, metastasis, drug resistance, and poor prognosis, necessitating the development of reagents for unambiguous detection of CSC- and EMT-associated proteins in tumor specimens. To this end, we generated novel antibodies to EMT- and CSC-associated proteins, including Goosecoid, Sox9, Slug, Snail, and CD133. Importantly, unlike several widely used antibodies to CD133, the anti-CD133 antibodies we generated recognize epitopes distal to known glycosylation sites, enabling analyses that are not confounded by differences in CD133 glycosylation. For all target proteins, we selected antibodies that yielded the expected target protein molecular weights by Western analysis and the correct subcellular localization patterns by immunofluorescence microscopy assay (IFA); binding selectivity was verified by immunoprecipitation-mass spectrometry and by immunohistochemistry and IFA peptide blocking experiments. Finally, we applied these reagents to assess modulation of the respective markers of EMT and CSCs in xenograft tumor models by IFA. We observed that the constitutive presence of human hepatocyte growth factor (hHGF) in the tumor microenvironment of H596 non-small cell lung cancer tumors implanted in homozygous hHGF knock-in transgenic mice induced a more mesenchymal-like tumor state (relative to the epithelial-like state when implanted in control SCID mice), as evidenced by the elevated expression of EMT-associated transcription factors detected by our novel antibodies. Similarly, our new anti-CD133 antibody enabled detection and quantitation of drug-induced reductions in CD133-positive tumor cells following treatment of SUM149PT triple-negative breast cancer xenograft models with the CSC/focal adhesion kinase (FAK) inhibitor VS-6063. Thus, our novel antibodies to CSC- and EMT-associated factors exhibit sufficient sensitivity and selectivity for immunofluorescence microscopy studies of these processes in preclinical xenograft tumor specimens and the potential for application with clinical samples.

Science & Technology - Other Topics↗
DOE OSTI2021

Global patterns of forest autotrophic carbon fluxes

Carbon (C) fixation, allocation, and metabolism by trees set the basis for energy and material flows in forest ecosystems and define their interactions with Earth’s changing climate. However, we lack a cohesive synthesis on how forest carbon fluxes vary globally with respect to climate and one another. Here, we draw upon 1,319 records from the Global Forest Carbon Database (ForC), representing all major forest types and the nine most significant autotrophic carbon fluxes, to comprehensively explore how C cycling in mature, undisturbed forests varies with latitude and climate on a global scale. We show that, across all flux variables analyzed, C cycling decreases continuously with absolute latitude – a finding that confirms multiple previous studies but contradicts the idea that net primary productivity of temperate forests rivals that of tropical forests. C flux variables generally displayed similar trends across latitude and multiple climate variables, with no differences in allocation detected at this global scale. Temperature variables in general, and mean annual temperature and temperature seasonality in particular, were the best univariate predictors of C flux, explaining 19 - 71% of variation in the C fluxes analyzed. The effects of temperature were modified by moisture availability, with C flux reduced under hot and dry conditions and sometimes under very high precipitation. C fluxes increased with growing season length, but this was never the best univariate predictor. Within the growing season, the influence of climate on C cycling was small but significant for a number of flux variables. These findings clarify how forest C flux varies with latitude and climate on a global scale. In a period of accelerating climatic change, this improved understanding of the fundamental climatic controls on forest C cycling sets a foundation for understanding patterns of change.

Banbury Morgan, Rebecca↗
DOE OSTI2024

Hydrogen Leak Modeling for Development of Smart Distributed Monitoring Under Unintended Releases

Hydrogen is a versatile and clean energy carrier that can be produced from various renewable sources such as wind, solar, and hydropower. Hydrogen has the potential to play a crucial role in decarbonizing industrial processes that are currently reliant on fossil fuels and provide long-duration and/or seasonal energy storage to enable electricity decarbonization. Hydrogen can also be used as a fuel for fuel cell vehicles, providing a zero-emission alternative to traditional internal combustion engines. DOE launched the Hydrogen Energy Earthshot (Hydrogen Shot) in June 2021 to reduce the cost of clean hydrogen by 80% to $1 per 1 kilogram in 1 decade ("1 1 1"). While promising, Hydrogen is highly-flammable, and in the presence of oxygen, it can form explosive mixtures. . Therefore, understanding leak scenarios is essential to evaluate and mitigate the safety risks associated with potential hydrogen leaks. An increased understanding of leak behavior, and having tools to model leaks, can help assess how hydrogen would disperse in different environments, influencing emergency response plans and safety measures, and identify potential issues with materials and design systems that can withstand the challenges posed by hydrogen. Recently, researchers have attempted to study hydrogen leaks for development of risk management strategies. However, the focus has been on closed or semi-closed spaces like storage rooms, vehicles, garages, and fueling stations - all promising locations for future hydrogen infrastructure. In this presentation, the modeling environment extends the span of research further by modeling hydrogen leak in an outdoor, open space. We will present the key challenges with modeling hydrogen leaks in an uncontrollable environment, how they were handled, and how modeling results informed sensor selection and placement. A Hydrogen research facility at the National Renewable Energy Laboratory (NREL) was used as a case study to model hydrogen leaks. In the future, Hydrogen wide area detection methodologies will be developed and tested at this site to monitor for unintended and operational hydrogen releases. The data generated from modeling will be used to develop a predictive model to detect hydrogen leak location based on concentration measured by sensors in this open space. Furthermore, the facility was also chosen because controlled hydrogen releases can be performed. A computational fluid dynamics (CFD) based modeling approach was taken to model hydrogen leak. The full-scale hydrogen facility was modeled with a large ambient domain. The electrolyzer at the facility can produce a controlled release rate of 27 kg-H2/hr. Site-specific atmospheric and weather condition data such as wind direction, wind speed at various altitudes, and temperature were used as inputs to the model. To capture the variability of weather conditions, a subset of the weather conditions experienced during daytime hours without precipitation over the course of three months was generated; using established data clustering techniques, a total of 100 condition sets were chosen. The results show statistical distributions and ranges of hydrogen concentrations at locations throughout the domain. These distributions are compared to experimental data from a constant mass flow, controlled hydrogen release at the facility. The stochastic wind conditions of the release make direct validation difficult, therefore, statistical comparison approaches were used. Wind conditions are found to significantly impact the release behavior, including direction and concentration. Sensor selection and placement is proposed for the facility and is now based on release behavior predicted for the facility given its weather patterns; this is much more informed than without the modeling results. The methodology and analysis procedure can be translated to other facilities using modified geometries and site-specific weather conditions. Hydrogen holds great promise as a renewable energy fuel, but ensuring safety in its production, storage, and use is paramount. Studying potential leak scenarios in an open space will help develop sensors to detect hydrogen on a large spectrum of concentration and eventually build a smart distributed monitoring system.

CFD↗
DOE OSTI2025

Leveraging large language models to automate the identification of healthcare access barriers for veterans

Objective: To develop and evaluate an automated system for identifying healthcare barriers focusing on transportation issues in veterans’ clinical notes using large language models (LLMs) and to assess the impact of different prompting strategies on classification performance and explanation consistency. Methods: We developed a hybrid system combining pattern matching for templated notes with LLM analysis for free-text notes. Using 2000 manually annotated clinical notes, we compared four prompting strategies (dual-role short, dual-role long, analysis-first, analysis-only) across Mistral-7B and Llama-3.1 models. We evaluated classification performance using standard metrics and assessed explanation consistency through embedding similarity analysis. Results: The analysis-first strategy achieved superior performance, with Mistral-7B reaching an F1 score of 0.914, outperforming traditional machine learning approaches (GBM: 0.786, BERT: 0.811). LLMs demonstrated higher explanation consistency within models (mean cosine similarity 0.887–0.908) compared to cross-model similarities (0.767–0.872). Pattern matching successfully handled 6.7% of templated notes deterministically. Mistral-7B showed greater internal consistency but higher abstention rates compared to Llama-3.1. Conclusion: Requiring LLMs to analyze evidence before classification improves both accuracy and explanation consistency for identifying transportation barriers in clinical notes. This approach enables automated barrier detection at scale while providing clinically relevant explanations, supporting both population-level healthcare planning and individual patient care decisions.

Healthcare access barriers↗
DOE OSTI2025

Human in vitro metabolism of an environmental mixture of polycyclic aromatic hydrocarbons (PAH) found at the Portland Harbor Superfund Site

Polycyclic aromatic hydrocarbons (PAHs) are widespread environmental contaminants that pose health risks to humans. Toxicity testing approaches of PAHs have evolved from traditional rodent models to New Approach Methodologies (NAMs), such as high-throughput screening in zebrafish, enabling rapid evaluation of chemical hazards. However, translating toxicity findings from laboratory systems to humans remains difficult due to complexity and species-specific differences. Chemical dosimetry modeling offers a quantitative framework to bridge this gap, but its accuracy depends on robust knowledge of PAH metabolism. The objective of this study was to measure human metabolism rates of Supermix-10, the ten most abundant PAHs found at the Portland Harbor Superfund Site, to support development of human pharmacokinetic models. We incubated individual PAHs from Supermix-10 in pooled human liver microsomes and quantified parent PAH disappearance using high-performance liquid chromatography (HPLC) with UV and florescent detection. To assess the potential of mixture interactions, we also measured metabolism of all 10 compounds in an equimolar mixture and compared rates of parent disappearance to those observed for individual PAHs. All Supermix-10 PAHs demonstrated rapid parent compound disappearance in human hepatic microsomes. PAHs grouped into three metabolism patterns: high metabolism rates and capacity (2-methylnaphthalene, acenaphthylene, fluorene, naphthalene), high affinity metabolism that rapidly achieves low-level saturation (benzo[a]anthracene, chrysene), and moderate metabolism rates and capacity (fluoranthene, pyrene, retene, phenanthrene). Smaller PAHs exhibited faster metabolism, and higher metabolism rates correlated inversely with molecular weight. When incubated in an equimolar mixture, Supermix-10 demonstrated significantly slower metabolism (47–89 %) compared to metabolism of individual PAHs at the same concentration. These findings enhance our understanding of PAH metabolism in humans and demonstrate significant mixture interactions under the conditions tested. Furthermore, our findings offer insights into the metabolic behavior of Supermix-10 and provide critical metabolism rate data to support the development of physiological based pharmacokinetic (PBPK) models. Dosimetry models can translate PAH chemical dosimetry from high-throughput testing platforms, like zebrafish and cellular system assays, to human exposures enhancing the accuracy and reliability of PAH risk assessments.

2-methylnaphthalene↗
DOE OSTI2015

A spectroscopic study of the extreme black widow PSR J1311–3430

We report on a series of spectroscopic observations of PSR J1311–3430, an extreme black-widow gamma-ray pulsar with a helium-star companion. In a previous study we estimated the neutron star mass as M{sub NS}=2.68±0.14 M{sub ⊙} (statistical error), based on limited spectroscopy and a basic (direct heating) light-curve model; however, much larger model-dependent systematics dominate the mass uncertainty. Our new spectroscopy reveals a range of complex source behavior. The variable He i companion wind emission lines can dominate broadband photometry, especially in red filters or near minimum brightness, and the wind flux should complete companion evaporation in a spin-down time. The heated companion face also undergoes dramatic flares, reaching ∼40,000 K over ∼20% of the star; this is likely powered by a magnetic field generated in the companion. The companion center-of-light radial velocity is now well measured with K{sub CoL}=615.4±5.1 km s{sup −1}. We detect non-sinusoidal velocity components due to the heated face flux distribution. Using our spectra to excise flares and wind lines, we generate substantially improved light curves for companion continuum fitting. We show that the inferred inclination and neutron star mass, however, remain sensitive to the poorly constrained heating pattern. The neutron star’s mass, M{sub NS}, is likely less than the direct heating value and could range as low as 1.8 M{sub ⊙} for extreme equatorial heating concentration. While we cannot yet pin down M{sub NS}, our data imply that an intrabinary shock reprocesses the pulsar emission and heats the companion. Improved spectra and, especially, models that include such shock heating are needed for precise parameter measurement.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

2024 Results for Avian Monitoring at the Technical Area 36 Minie Site, Technical Area 39 Point 6, Technical Area 16 Burn Ground, and DARHT at Los Alamos National Laboratory

Los Alamos National Laboratory (LANL) biological subject matter experts in the Environmental Protection and Compliance Division initiated a multi-year program in 2013 to monitor avifauna (birds) at two open detonation sites and one open burn site on LANL property. Additional monitoring began in 2017 at a third firing site, the Dual-Axis Radiographic Hydrodynamic Test (DARHT) Facility. In this annual report, we compare monitoring results from these efforts among years to identify and evaluate firing and open burn site impacts on the local bird community. The objectives of this study are • to determine whether LANL operations impact bird abundance, species richness, or diversity; • to examine occupancy and nest success of secondary-cavity nesting birds that use nest boxes; and • to examine chemical concentrations (such as radionuclides, inorganic elements, and/or organic compounds) in nonviable eggs and deceased nestlings that are collected opportunistically with the upper-level bounds of background concentrations, when available. During May through July 2024, LANL biologists completed multiple avian point count surveys at each of the following treatment sites: • Technical Area (TA) 36 Minie Site, • TA-39 Point 6, • TA-16 Burn Ground, and • DARHT. We recorded a total of 1,088 birds that represented 65 species at the four treatment sites and compared these results with data from their associated control sites. In 2024, abundance and species richness at treatment and control sites continued to trend similarly from year to year, with minor random deviations expected from bird communities. Species richness at firing sites differed little from the previous year’s values. Two new bird species were observed at the firing sites—cedar waxwing (Bombycilla cedrorum) and pinyon jay (Gymnorhinus cyanocephalus). Shannon diversity values at TA-36 Minie Site, TA-39, and DARHT were statistically higher than one or more of their associated controls. Annual species diversity at treatment sites was high in 2024 across all firing sites relative to similar habitat control sites. We also monitored avian nest boxes to compare occupancy and nest success data from nest boxes at treatment sites with the overall avian nest box monitoring network and against a subset of relevant control sites. Nest box success has decreased at both treatment and control sites since monitoring began, suggesting that overlapping climatic factors are responsible for patterns of declining nest success. In 2024, nonviable avian eggs and one nestling were opportunistically collected at Bandelier National Monument, TA-16 Burn Ground, TA-36 Minie, TA-39 Point 6, and DARHT. All egg samples and the one nestling sample were evaluated for per- and polyfluoroalkyl substances, which were detected from all locations, including the control site at Bandelier National Monument. Overall results from 2024 continue to suggest that operations at the four treatment sites are not negatively impacting bird populations. This long-term project will continue to monitor for any changes over time.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Radio Morphology of Red Geysers

We present 150 MHz, 1.4 GHz, and 3 GHz radio imaging (LoTSS, FIRST, and VLASS) and spatially resolved ionized gas characteristics (SDSS IV-MaNGA) for 140 local ($z$ < 0.1) early-type red geyser galaxies. These galaxies have a low star formation activity (with a star formation rate, SFR, ~ 0.01 $M$ ⊙ yr -1 ) but show unique extended patterns in spatially resolved emission-line maps that have been interpreted as large-scale ionized winds driven by active galactic nuclei (AGN). In this work, we confirm that red geysers host low-luminosity radio sources ($L$ 1.4GHz ~ 10 22 $WHz$ -1 ). Out of 42 radio-detected red geysers, 32 are spatially resolved in LoTSS and FIRST, with radio sizes varying between ~5–25 kpc. Three sources have radio sizes exceeding 40 kpc. A majority display a compact radio morphology and are consistent with either low-power compact radio sources (FR0 galaxies) or radio-quiet quasars. They may be powered by small-scale AGN-driven jets that remain unresolved at the current 5'' resolution of radio data. The extended radio sources, not belonging to the "compact" morphological class, exhibit steeper spectra with a median spectral index of -0.67, indicating the dominance of lobed components. Furthermore, the red geysers hosting extended radio sources also have the lowest specific SFRs, suggesting they either have a greater impact on the surrounding interstellar medium or are found in more massive halos on average. The degree of alignment of the ionized wind cone and the extended radio features are either 0° or 90°, indicating possible interaction between the interstellar medium and the central radio AGN.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

A cognitive electrophysiological signature differentiates amnestic mild cognitive impairment from normal aging

Background: Noninvasive and effective biomarkers for early detection of amnestic mild cognitive impairment (aMCI) before measurable changes in behavioral performance remain scarce. Cognitive event-related potentials (ERPs) measure synchronized synaptic neural activity associated with a cognitive event. Loss of synapses is a hallmark of the neuropathology of early Alzheimer’s disease (AD). In the present study, we tested the hypothesis that ERP responses during working memory retrieval discriminate aMCI from cognitively normal controls (NC) matched in age and education. Methods: Eighteen NC, 17 subjects with aMCI, and 13 subjects with AD performed a delayed match-to-sample task specially designed not only to be easy enough for impaired participants to complete but also to generate comparable performance between subjects with NC and those with aMCI. Scalp electroencephalography, memory accuracy, and reaction times were measured. Results: Whereas memory performance separated the AD group from the others, the performance of NC and subjects with aMCI was similar. In contrast, left frontal cognitive ERP patterns differentiated subjects with aMCI from NC. Enhanced P3 responses at left frontal sites were associated with nonmatching relative to matching stimuli during working memory tasks in patients with aMCI and AD, but not in NC. The accuracy of discriminating aMCI from NC was 85% by using left frontal match/nonmatch effect combined with nonmatch reaction time. Conclusions: The left frontal cognitive ERP indicator holds promise as a sensitive, simple, affordable, and noninvasive biomarker for detection of early cognitive impairment.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations

Abstract Background Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in peatlands underlain with permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland in northern Minnesota (the SPRUCE whole-ecosystem warming experiment and surrounding bog) were analyzed for dsDNA viral community ecological patterns, and the recovered viral populations (vOTUs) were compared with our curated PIGEON database of 266,125 vOTUs from diverse ecosystems. Results Within the SPRUCE experiment, viral community composition was significantly correlated with peat depth, water content, and carbon chemistry, including CH 4 and CO 2 concentrations, but not with temperature during the first 2 years of warming treatments. Peat vOTUs with aquatic-like signatures (shared predicted protein content with marine and/or freshwater vOTUs) were significantly enriched in more waterlogged surface peat depths. Predicted host ranges for SPRUCE vOTUs were relatively narrow, generally within a single bacterial genus. Of the 4326 SPRUCE vOTUs, 164 were previously detected in other soils, mostly peatlands. None of the previously identified 202,371 marine and freshwater vOTUs in our PIGEON database were detected in SPRUCE peat, but 0.4% of 80,714 viral clusters (VCs, grouped by predicted protein content) were shared between soil and aquatic environments. On a per-sample basis, vOTU recovery was 32 times higher from viromes compared with total metagenomes. Conclusions Results suggest strong viral “species” boundaries between terrestrial and aquatic ecosystems and to some extent between peat and other soils, with differences less pronounced at higher taxonomic levels. The significant enrichment of aquatic-like vOTUs in more waterlogged peat suggests that viruses may also exhibit niche partitioning on more local scales. These patterns are presumably driven in part by host ecology, consistent with the predicted narrow host ranges. Although more samples and increased sequencing depth improved vOTU recovery from total metagenomes, the substantially higher per-sample vOTU recovery after viral particle enrichment highlights the utility of soil viromics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Comparison of multiple tau-PET measures as biomarkers in aging and Alzheimer's disease

The recent development of tau-specific positron emission tomography (PET) tracers enables in vivo quantification of regional tau pathology, one of the key lesions in Alzheimer's disease (AD). Tau PET imaging may become a useful biomarker for clinical diagnosis and tracking of disease progression but there is no consensus yet on how tau PET signal is best quantified. The goal of the current paper was to evaluate multiple whole-brain and region-specific approaches to detect clinically relevant tau PET signal. Two independent cohorts of cognitively normal adults and amyloid-positive (Aβ + ) patients with mild cognitive impairment (MCI) or AD-dementia underwent [ 18 F]AV-1451 PET. Methods for tau tracer quantification included: (i) in vivo Braak staging, (ii) regional uptake in Braak composite regions, (iii) several whole-brain measures of tracer uptake, (iv) regional uptake in AD-vulnerable voxels, and (v) uptake in a priori defined regions. Receiver operating curves characterized accuracy in distinguishing Aβ - controls from AD/MCI patients and yielded tau positivity cutoffs. Clinical relevance of tau PET measures was assessed by regressions against cognition and MR imaging measures. Key tracer uptake patterns were identified by a factor analysis and voxel-wise contrasts. Braak staging, global and region-specific tau measures yielded similar diagnostic accuracies, which differed between cohorts. While all tau measures were related to amyloid and global cognition, memory and hippocampal/entorhinal volume/thickness were associated with regional tracer retention in the medial temporal lobe. Key regions of tau accumulation included medial temporal and inferior/middle temporal regions, retrosplenial cortex, and banks of the superior temporal sulcus. Finally, our data indicate that whole-brain tau PET measures might be adequate biomarkers to detect AD-related tau pathology. However, regional measures covering AD-vulnerable regions may increase sensitivity to early tau PET signal, atrophy and memory decline.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff

Teff (Eragrostis tef) is a cornerstone of food security in the Horn of Africa, where it is prized for stress resilience, grain nutrition, and market value. Here, we report a chromosome-scale assembly of allotetraploid teff (variety Dabbi) and patterns of subgenome dynamics. The teff genome contains two complete sets of homoeologous chromosomes, with most genes maintaining as syntenic gene pairs. TE analysis allows us to estimate that the teff polyploidy event occurred ~1.1 million years ago (mya) and that the two subgenomes diverged ~5.0 mya. Despite this divergence, we detect no large-scale structural rearrangements, homoeologous exchanges, or biased gene loss, in contrast to many other allopolyploids. The two teff subgenomes have partitioned their ancestral functions based on divergent expression across a diverse expression atlas. Together, these genomic resources will be useful for accelerating breeding of this underutilized grain crop and for fundamental insights into polyploid genome evolution.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Vehicle track segmentation using higher order random fields

Here, we present an approach to segment vehicle tracks in coherent change detection images, a product of combining two synthetic aperture radar images taken at different times. The approach uses multiscale higher order random field models to capture track statistics, such as curvatures and their parallel nature, that are not currently utilized in existing methods. These statistics are encoded as 3-by-3 patterns at different scales. The model can complete disconnected tracks often caused by sensor noise and various environmental effects. Coupling the model with a simple classifier, our approach is effective at segmenting salient tracks. We improve the F-measure on a standard vehicle track data set to 0.963, up from 0.897 obtained by the current state-of-the-art method.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

Hanford Tank Waste Particle Atlas

Several methods have been utilized to perform solid phase characterization. Polarized light microscopy (PLM) is used to identify individual particles based on size, shape, color, and optical properties (e.g., refractive index1, birefringence, extinction positions, and interference figures). Scanning electron microscopy with energy-dispersive spectroscopy (SEM/EDS) is used to detect which elements are present in individual particles and to infer chemical phase identification based on the metals present in combination with the size and shape of the particles. Powder X-ray diffraction (XRD) is used to identify crystalline phases present in bulk samples by matching the X-ray patterns with a library of known patterns for pure phases. Transmission electron microscopy (TEM) is used to identify individual particles by their X-ray diffraction patterns. RAMAN analysis is used to identify bulk sample compositions by matching RAMAN spectra with a library of known patterns. Other specialized techniques have not been employed routinely for Hanford tank waste samples.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2020

TriC: Distributed-memory Triangle Counting by Exploiting the Graph Structure

Graph analytics has emerged as an important tool in the analysis of large scale data from diverse application domains such as social networks, cyber security and bioinformatics. Counting the number of triangles in a graph is a fundamental kernel with several applications such as detecting the community structure of a graph or in identifying important vertices in a graph. The ubiquity of massive datasets is driving the need to scale graph analytics on parallel systems. However, numerous challenges exist in efficiently parallelizing graph algorithms, especially on distributed-memory systems. Irregular memory accesses and communication patterns, low computation to communication ratios, and the need for frequent synchronization are some of the leading challenges. In this paper, we present TriC, our distributed-memory implementation of triangle counting in graphs using the Message Passing Interface (MPI), as a submission to the 2020 GraphChallenge competition. Using a set of synthetic and real-world inputs from the challenge, we demonstrate a speedup of up to 90x relative to previous work on 32 processor-cores of a NERSC Cori node. We also provide details from distributed runs with up to8192 processes along with strong scaling results. The observations presented in this work provide an understanding of the system-level bottlenecks at scale that specifically impact sparse-irregular workloads and will therefore benefit other efforts to parallelize graph algorithms.

Halappanavar, Mahantesh↗